+Open data
-Basic information
Entry | Database: PDB / ID: 1a4j | ||||||
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Title | DIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR | ||||||
Components |
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Keywords | IMMUNOGLOBULIN / ANTIBODY / CATALYTIC ANTIBODY / DIELS ALDER / GERMLINE | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Potential therapeutics for SARS / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Spiller, B.W. / Romesburg, F.E. / Schultz, P.G. / Stevens, R.C. | ||||||
Citation | Journal: Science / Year: 1998 Title: Immunological origins of binding and catalysis in a Diels-Alderase antibody. Authors: Romesberg, F.E. / Spiller, B. / Schultz, P.G. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a4j.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a4j.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a4j_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 1a4j_full_validation.pdf.gz | 488.6 KB | Display | |
Data in XML | 1a4j_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 1a4j_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a4j ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a4j | HTTPS FTP |
-Related structure data
Related structure data | 1a4kSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23706.475 Da / Num. of mol.: 2 / Fragment: FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 25F2 / Plasmid: P4XH / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: UniProt: P01834 #2: Antibody | Mass: 23593.459 Da / Num. of mol.: 2 / Fragment: FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 25F2 / Plasmid: P4XH / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 51.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 19% PEG 8K, 20% GLYCEROL, 200MM MG(CH3COO)2, 10MM CDS04 100MM BISTRIS PH 6.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: WIGGLER |
Radiation | Monochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 63217 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.044 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.27 / % possible all: 95.4 |
Reflection | *PLUS Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 95.4 % / Rmerge(I) obs: 0.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A4K Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 36.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.245 |